Fix merge conflicts

Author: jderouillat

.gitlab-ci.yml

@@ -6,7 +6,7 @@ compile:
   stage: compile
   only:
     - develop
-    - envelope_cylindrical
+    - smilei_Poisson_AM
 
   script:
     # Force workdir cleaning in case of retried
@@ -28,7 +28,7 @@ makerun1D:
   stage: makerun
   only:
     - develop
-    - envelope_cylindrical
+    - smilei_Poisson_AM
 
   script:
     # Move in test dir
@@ -40,7 +40,7 @@ makerun2D:
   stage: makerun
   only:
     - develop
-    - envelope_cylindrical
+    - smilei_Poisson_AM
 
   script:
     # Move in test dir
@@ -52,7 +52,7 @@ makerun3D:
   stage: makerun
   only:
     - develop
-    - envelope_cylindrical
+    - smilei_Poisson_AM
 
   script:
     # Move in test dir
@@ -64,7 +64,7 @@ makerunAM:
   stage: makerun
   only:
     - develop
-    - envelope_cylindrical
+    - smilei_Poisson_AM
 
   script:
     # Move in test dir
@@ -76,7 +76,7 @@ makerunV:
   stage: makerun
   only:
     - develop
-    - envelope_cylindrical
+    - smilei_Poisson_AM
 
   script:
     # Move in test dir
@@ -88,7 +88,7 @@ makerunCollisions:
   stage: makerun
   only:
     - develop
-    - envelope_cylindrical
+    - smilei_Poisson_AM
 
   script:
     # Move in test dir

doc/Sphinx/namelist.rst

@@ -127,11 +127,11 @@ The block ``Main`` is **mandatory** and has the following syntax::
 
   .. warning::
 
-    The ``"AMcylindrical"`` geometry is currently proposed in beta version.
+    The ``"AMcylindrical"`` geometry has some restrictions.
     Boundary conditions must be set to ``"remove"`` for particles,
     ``"silver-muller"`` for longitudinal EM boundaries and
     ``"buneman"`` for transverse EM boundaries.
-    Vectorization, collisions, scalar diagnostics, Poisson solver and
+    Vectorization, collisions, scalar diagnostics and
     order-4 interpolation are not supported yet.
 
 .. py:data:: interpolation_order
@@ -643,9 +643,9 @@ Each species has to be defined in a ``Species`` block::
 
    :type: A python list of integers.
 
+   This list sets the number of evenly spaced particles per cell per dimension at their initial positions.
    The size of the list must be the simulation particle dimension. It can be used only if `position_initialization` is set to `regular`.
    The product of the elements of the provided list must be equal to `particles_per_cell`.
-   This list sets the number of evenly spaced particles per cell per dimension at their initial positions.
    The numbers are given in the order [`Nx`, `Ny`, `Nz`] in cartesian geometries and [`Nx`, `Nr`, `Ntheta`] in `AMcylindrical` in which
    case we advise to use :math:`Ntheta \geq  4\times (number\_of\_AM-1)`.
 
@@ -1024,7 +1024,11 @@ Each particle injector has to be defined in a ``ParticleInjector`` block::
     :default:  ``tconstant()``
 
     The temporal envelope of the injector.
-     
+    
+----
+
+.. rst-class:: experimental
+
 .. _Particle_merging:
 
 Particle Merging
@@ -2491,7 +2495,9 @@ This is done by including a block ``DiagFields``::
   In ``AMcylindrical`` geometry, the ``x``, ``y`` and ``z``
   indices are replaced by ``l`` (longitudinal), ``r`` (radial) and ``t`` (theta). In addition,
   the angular Fourier modes are denoted by the suffix ``_mode_i`` where ``i``
-  is the mode number. In summary, the list of fields reads as follows.
+  is the mode number.
+  If a field is specified without its associated mode number, all available modes will be included.
+  In summary, the list of fields reads as follows.
 
   .. rst-class:: nowrap
 

doc/Sphinx/releases.rst

@@ -9,14 +9,16 @@ get the latest version of Smilei on `GitHub <https://github.com/SmileiPIC/Smilei
 Upcoming changes
 ^^^^^^^^^^^^^^^^
 
-* Interface with the PICSAR library (currently experimental)
-* Particle merging (beta version)
-* Additional prescribed fields that only contribute to pushing particles
-* More control over the moving window movement
-* More control over the regular position initialization in Cartesian geometries
-* AMcylindrical now supports almost all features of the code (Poisson solver and scalar diags still missing)
-* Bugfix: particle binning was not following the moving window
-* Bugfix: gaussian profile with order 0 was incorrect
+* Already available, but experimental:
+
+  * Particle merging
+  * Nuclear reactions
+  * Interface with the PICSAR library for AM spectral solver
+
+* In the future:
+
+  * Single Domain Multiple Decomposition
+  * Additional prescribed fields that only contribute to pushing particles
 
 ----
 
@@ -30,27 +32,51 @@ The latest version tarball can be donwloaded here:
 **Download**: `Smilei latest <_downloads/Smilei.tar.gz>`_
 
 
+----
+
+Release 4.3
+^^^^^^^^^^^^^^^^^^^^^
+
+**Download**: `Smilei v4.3 <_downloads/smilei-v4.3.tar.gz>`_
+
+
+* ``AMcylindrical`` : envelope, ionization, additional diagnotics,
+  number of ppc per direction, binomial current filter, poisson solver,
+  non-separable laser initialization per mode, improved diag field nomenclature
+* Particle injector
+* More control over the moving window movement
+* More control over the regular position initialization in Cartesian geometries
+* Bugfixes:
+
+ * ionization of frozen species
+ * particle binning was not following the moving window
+ * gaussian profile with order 0 was incorrect
+ * tracked particles post-processing was incorrect above 20M particles
+ * better management of particle binning in collisions
+ * Intel 19 optimizations
+
+
 ----
 
 Release 4.2
 ^^^^^^^^^^^^^^^^^^^^^
 
 **Download**: `Smilei v4.2 <_downloads/smilei-v4.2.tar.gz>`_
 
-
+* ``AMcylindrical`` geometry with azimuthal Fourier decomposition (beta version)
 * Different convention for circular polarization amplitude
-* Binomial filter in Cartesian 3D bug fix in parallel implementation
 * 1D and 2D laser envelope model
-* Cylindrical geometry with azimuthal Fourier decomposition (beta version)
 * Compatibility between various ionization and QED models
 * Bugfixes:
-   * Various crashes linked to vectorization
-   * `LaserGaussian2D` when focused far from boundary
-   * Laser :py:data:`a0` normalization to :py:data:`omega`
-   * Frozen particles are now properly ionized
-   * Position initialization over another species with moving window
-   * Tracked particles output was missing the mass factor for momenta
-   * Breit-Wheeler pair production with fine grain sorted particles
+
+  * Binomial filter in Cartesian 3D parallel implementation
+  * Various crashes linked to vectorization
+  * ``LaserGaussian2D`` when focused far from boundary
+  * Laser :py:data:`a0` normalization to :py:data:`omega`
+  * Frozen particles are now properly ionized
+  * Position initialization over another species with moving window
+  * Tracked particles output was missing the mass factor for momenta
+  * Breit-Wheeler pair production with fine grain sorted particles
 
 
 ----
@@ -67,11 +93,13 @@ Release 4.1
  * collisions (badly affected by vectorization)
  * adaptive vectorization with dynamic load balancing
  * memory leak in the laser envelope model
- 
-* Disable usage of `-ipo` to compile on supercomputers despite of saving time simulation
+
+* Disable usage of `-ipo` to compile on supercomputers
+  despite of saving time simulation
 
  * it needs too many resources (time and memory) to link
- * it is recommended to do some tests on a new supercomputer without and then to re-establish it
+ * it is recommended to do some tests on a new supercomputer
+   without and then to re-establish it
 
 .. warning::
 
@@ -102,7 +130,8 @@ Release 3.5
 **Download**: `Smilei v3.5 <_downloads/smilei-v3.5.tar.gz>`_
 
 * :doc:`Laser defined in tilted plane<laser_offset>`
-* Bugfixes: Field diagnostic subgrid, Scalar diagnostic PoyInst, MPI tags for large number of patches
+* Bugfixes: Field diagnostic subgrid, Scalar diagnostic PoyInst,
+  MPI tags for large number of patches
 
 ----
 
@@ -143,7 +172,8 @@ Release 3.3
 * QED radiation reaction
 * Monte-Carlo QED photon emission
 * *Test mode* to quickly check the namelist consistency
-* *ParticleBinning* and *Screen* diagnostics accept a python function as their ``deposited_quantity`` and ``axis``.
+* *ParticleBinning* and *Screen* diagnostics accept a python function as their
+  ``deposited_quantity`` and ``axis``.
 * Bugfixes: 4th order, field ionization
 
 ----
@@ -156,7 +186,8 @@ Release 3.2
 * New pushers (Vay's and Higuera-Cary's)
 * *Numpy* used for filtering track particles
 * Fourth order in 3D
-* Add some missing 3D features: external fields management, boundary conditions and non-neutral plasma initialization
+* Add some missing 3D features: external fields management, boundary conditions
+  and non-neutral plasma initialization
 * OpenMP support in moving window
 * Tracked particles post-processing improved for large files
 * Bugfixes: energy computation in 3D or with moving window, random number seed

doc/Sphinx/smilei_theme/static/smilei_theme.css_t

@@ -631,6 +631,18 @@ div.header > * {
 	font-size:1.3em;
 }
 
+div.experimental h2:first-of-type::after, dl.experimental dt:first-of-type::after {
+	content: "experimental";
+	background:red;
+	color:white;
+	margin: 0 10px;
+	padding: 0 5px;
+	border-radius: 5px;
+	font-size: 0.8em;
+	font-family: "BPreplay";
+	font-weight: bold;
+}
+
 /* --------------------------------------------------------------------*/
 /* Logos and icons */
 img.logo {

src/Diagnostic/DiagnosticFields.cpp

@@ -36,9 +36,24 @@ DiagnosticFields::DiagnosticFields( Params &params, SmileiMPI *smpi, VectorPatch
     // Extract the requested fields
     vector<string> fieldsToDump( 0 );
     PyTools::extract( "fields", fieldsToDump, "DiagFields", ndiag );
-    
+   
+    //Avoid modes repetition in the namelist by interpreting field quantity as all modes of this quantity
+    if (params.geometry == "AMcylindrical") {
+        vector<string> fieldsToAdd( 0 );
+        for (int ifield = 0; ifield < fieldsToDump.size(); ifield++){
+            if (fieldsToDump[ifield].find("_mode_") ==  std::string::npos) {
+                for (unsigned int imode = 1; imode < params.nmodes; imode ++){
+                    fieldsToAdd.push_back(fieldsToDump[ifield]+"_mode_"+to_string(imode));
+                }
+                fieldsToDump[ifield] = fieldsToDump[ifield] + "_mode_0" ;
+            }
+        }
+        for (int ifield = 0; ifield < fieldsToAdd.size(); ifield++){
+            fieldsToDump.push_back(fieldsToAdd[ifield]);
+        }
+    }
+ 
     // List all fields that are requested
-    std::vector<Field *> allFields( 0 );
     ostringstream ss( "" );
     fields_indexes.resize( 0 );
     fields_names  .resize( 0 );

src/Diagnostic/DiagnosticPerformances.cpp

@@ -201,7 +201,7 @@ void DiagnosticPerformances::run( SmileiMPI *smpi, VectorPatch &vecPatches, int
         double time = itime * timestep;
         for( unsigned int ipatch=0; ipatch < number_of_patches; ipatch++ ) {
             for( unsigned int ispecies = 0; ispecies < number_of_species; ispecies++ ) {
-                if( time < vecPatches( ipatch )->vecSpecies[ispecies]->time_frozen ) {
+                if( time < vecPatches( ipatch )->vecSpecies[ispecies]->time_frozen_ ) {
                     number_of_frozen_particles += vecPatches( ipatch )->vecSpecies[ispecies]->getNbrOfParticles();
                 } else {
                     number_of_particles += vecPatches( ipatch )->vecSpecies[ispecies]->getNbrOfParticles();

src/Ionization/IonizationFactory.h

@@ -30,7 +30,7 @@ class IonizationFactory
 
         } else if( model == "from_rate" ) {
 
-            if( species->max_charge > ( int )species->maximum_charge_state ) {
+            if( species->max_charge > ( int )species->maximum_charge_state_ ) {
                 ERROR( "For species '" << species->name_ << ": charge > maximum_charge_state" );
             }
 

src/Ionization/IonizationFromRate.cpp

@@ -15,8 +15,8 @@ IonizationFromRate::IonizationFromRate( Params &params, Species *species ) : Ion
 
     DEBUG( "Creating the FromRate Ionizaton class" );
 
-    maximum_charge_state_ = species->maximum_charge_state;
-    ionization_rate = species->ionization_rate;
+    maximum_charge_state_ = species->maximum_charge_state_;
+    ionization_rate_ = species->ionization_rate_;
 
     DEBUG( "Finished Creating the FromRate Ionizaton class" );
 
@@ -46,7 +46,7 @@ void IonizationFromRate::operator()( Particles *particles, unsigned int ipart_mi
         particleData.startAt( ipart_min );
         PyTools::setIteration( itime );
         particleData.set( particles );
-        ret = ( PyArrayObject * )PyObject_CallFunctionObjArgs( ionization_rate, particleData.get(), NULL );
+        ret = ( PyArrayObject * )PyObject_CallFunctionObjArgs( ionization_rate_, particleData.get(), NULL );
         PyTools::checkPyError();
         if( ret == NULL ) {
             ERROR( "ionization_rate profile has not provided a correct result" );

src/Ionization/IonizationFromRate.h

@@ -25,7 +25,7 @@ class IonizationFromRate : public Ionization
 
     int itime;
     unsigned int maximum_charge_state_;
-    PyObject *ionization_rate;
+    PyObject *ionization_rate_;
 
 };
 

src/MultiphotonBreitWheeler/MultiphotonBreitWheelerFactory.h

@@ -35,7 +35,7 @@ class MultiphotonBreitWheelerFactory
         MultiphotonBreitWheeler *Multiphoton_Breit_Wheeler_process = NULL;
 
         // Assign the correct Radiation model to Radiate
-        if( !species->multiphoton_Breit_Wheeler[0].empty() ) {
+        if( !species->multiphoton_Breit_Wheeler_[0].empty() ) {
             Multiphoton_Breit_Wheeler_process = new MultiphotonBreitWheeler( params, species );
             if( params.Laser_Envelope_model & species->ponderomotive_dynamics ) {
                 ERROR( "Multiphoton Breit-Wheeler model is not yet implemented for species interacting with Laser Envelope model." );